Classifies unknown transposable element (TE) consensus sequences into four categories, according to their mechanism of transposition: DNA transposons, Long Terminal Repeats (LTRs), Long Interspersed Nuclear Elements (LINEs), Short Interspersed Nuclear Elements (SINEs). TEclass uses support vector machines, random forests, learning vector quantisation, and also predicts Open Reading Frames (ORFs). TEclass is not a tool to annotate whole-genome data, thus it is not a replacement for RepeatMasker or Censor. Its primary purpose is to classify the repeat libraries which can subsequently be used by these two tools. Thus, the input should not contain more than a few thousand sequences.

[…] server. analysis of k-mer frequency distributions were done in jellyfish and the assembly of repeatable dna was done in tedna , the provisional classification of the assembled elements was done by teclass. all mapping and manipulation of genomic reads were done in clc genomics workbench., agata weydmann and artur burzyński contributed equally to this work., publisher's note: springer nature […]

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[…] server. analysis of k-mer frequency distributions were done in jellyfish and the assembly of repeatable dna was done in tedna , the provisional classification of the assembled elements was done by teclass. all mapping and manipulation of genomic reads were done in clc genomics workbench., agata weydmann and artur burzyński contributed equally to this work., publisher's note: springer nature […]

[…] or reduction in scaffold number., the assembled genomes were masked before gene prediction using a customized pipeline which included repeatmasker-open-3-3-0, repbase [], repeatscout [], trf [] and teclass []. fungal genes downloaded from ncbi (august, 2012) were mapped to the vi1 genome assembly using exonerate [] for similarity based gene prediction. transcriptome assemblies for in planta […]

[…] analysis, repeatmodeler [] was used to construct a te library. elements within the library were then classified using a homology search with repbase and a support vector machine (svm) method (teclass) []. a total of 44.3 % of the s. furcifera genome consists of tandem repeats and tes (table ); lower than the brown planthopper (48.6 %) but much higher than the pea aphid (33.3 %). class […]

[…] library of interspersed repeat families as input for repeatmasker []. repeatmasker was also used to find and mask genomic regions of low complexity. we applied the automated classification tool teclass [] to categorize the predicted repeat sequences into the four main transposable element categories dna transposon, long interspersed nuclear element (line), short interspersed nuclear element […]

[…] blastx with an e-value cutoff of 1e-06, and then the repeats containing hits to transposon related proteins were eliminated from the list of novel repeats. the novel repeats were classified using teclass [], and then were used as a custom library for repeatmasker to further mask repetitive sequences in the sweetpotato bess., the sweetpotato bess without known and novel repeats were analyzed […]

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